Okay I've found a workaround for the issue :
0/ Backup your user account !!!
1/ Stop Akonadi, Kontact, and the MySQL process launched by Akonadi.
2/ rm -rf ~/.config/akonadi
3/ rm -rf ~/.local/share/akonadi
4/ Restart Kontact
5/ Reconfigure the apps so that they correctly point to the folders and files 
where the data is.

Anyway this is not suitable in a production environment, and the fix
should be done. I point that the error occured after an upgrade from
Oneiric.

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https://bugs.launchpad.net/bugs/979211

Title:
  Kmail folders error

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